Hello all,

I'm curious about the logic used for column alignment when displaying
tabular files (which for me was the headline feature of the last
Galaxy Release - I'm very pleased to have this added at last).
https://bitbucket.org/galaxy/galaxy-central/issue/553

Quoting from templates/dataset/tabular_chunked.mako

        function renderCell(cell_contents, index, colspan){
            if (colspan !== undefined){
                return $('<td>').attr('colspan',
colspan).addClass('stringalign').text(cell_contents);
            }
            else if (DATASET_TYPES[index] == 'str'){
                /* Left align all str columns, right align the rest */
                return $('<td>').addClass('stringalign').text(cell_contents);;
            }
            else{
                return $('<td>').text(cell_contents);
            }
        }

It seems to me that the logic should be right align all numeric
columns, left align the rest. At very least, columns of type 'list'
should also be left aligned. Otherwise you can easily have a situation
where on clicking the "eye" you get an apparently empty dataset
(unless you scroll right or down).

This can easily happen with FASTA to tabular (default settings), where
the descriptions have commas in them (common with annotation) thus the
first column is considered to be a list (and the second column type
str for the sequence). If some of the later sequences in the file have
very long descriptions, right aligning the description column makes
the dataset appear empty.

I can provide a screen shot if it would help to explain, but here is
my proposed patch.

Regards,

Peter

--

$ hg diff templates/dataset/tabular_chunked.mako
diff -r 8657ada96fca templates/dataset/tabular_chunked.mako
--- a/templates/dataset/tabular_chunked.mako    Fri Jun 15 16:05:48 2012 +0100
+++ b/templates/dataset/tabular_chunked.mako    Mon Jun 18 16:23:44 2012 +0100
@@ -17,8 +17,8 @@
             if (colspan !== undefined){
                 return $('<td>').attr('colspan',
colspan).addClass('stringalign').text(cell_contents);
             }
-            else if (DATASET_TYPES[index] == 'str'){
-                /* Left align all str columns, right align the rest */
+            else if (DATASET_TYPES[index] == 'str' ||
DATASET_TYPES[index] == 'list'){
+                /* Left align all str and list columns, right align the rest */
                 return $('<td>').addClass('stringalign').text(cell_contents);;
             }
             else{
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